3KQ4

Structure of Intrinsic Factor-Cobalamin bound to its receptor Cubilin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Transcobalamin C-terminal domain-like	8051863	3002041	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Six-hairpin glycosidases	8051862	3000970	SCOP2B (2022-06-29)
C	SCOP2 Family	Transcobalamin C-terminal domain-like	8050039	4006739	SCOP2 (2022-06-29)
C	SCOP2 Family	Transcobalamin N-terminal domain-like	8048589	4006152	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Transcobalamin C-terminal domain-like	8051863	3002041	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Six-hairpin glycosidases	8051862	3000970	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	Transcobalamin C-terminal domain-like	8051863	3002041	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Six-hairpin glycosidases	8051862	3000970	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Cobalamin_bind	e3kq4A1	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: Cobalamin_bind	ECOD (1.6)
A	DUF4430	e3kq4A2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DUF4430	ECOD (1.6)
C	Cobalamin_bind	e3kq4C3	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: Cobalamin_bind	ECOD (1.6)
C	DUF4430	e3kq4C2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DUF4430	ECOD (1.6)
E	Cobalamin_bind	e3kq4E3	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: Cobalamin_bind	ECOD (1.6)
E	DUF4430	e3kq4E2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DUF4430	ECOD (1.6)
D	CUB	e3kq4D2	A: beta sandwiches	X: jelly-roll	H: Spermadhesin, CUB domain (From Topology)	T: Spermadhesin, CUB domain	F: CUB	ECOD (1.6)
B	CUB	e3kq4B2	A: beta sandwiches	X: jelly-roll	H: Spermadhesin, CUB domain (From Topology)	T: Spermadhesin, CUB domain	F: CUB	ECOD (1.6)
F	CUB	e3kq4F2	A: beta sandwiches	X: jelly-roll	H: Spermadhesin, CUB domain (From Topology)	T: Spermadhesin, CUB domain	F: CUB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)
A	2.170.130.30	Mainly Beta	Beta Complex	Ferric Hydroxamate Uptake Protein	Chain A, domain 1	CATH (4.3.0)
C	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)
C	2.170.130.30	Mainly Beta	Beta Complex	Ferric Hydroxamate Uptake Protein	Chain A, domain 1	CATH (4.3.0)
E	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)
E	2.170.130.30	Mainly Beta	Beta Complex	Ferric Hydroxamate Uptake Protein	Chain A, domain 1	CATH (4.3.0)
D	2.60.120.290	Mainly Beta	Sandwich	Jelly Rolls	Spermadhesin, CUB domain	CATH (4.3.0)
B	2.60.120.290	Mainly Beta	Sandwich	Jelly Rolls	Spermadhesin, CUB domain	CATH (4.3.0)
F	2.60.120.290	Mainly Beta	Sandwich	Jelly Rolls	Spermadhesin, CUB domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF01122	Eukaryotic cobalamin-binding protein (Cobalamin_bind)	Eukaryotic cobalamin-binding protein	-	Repeat
B, D, F	PF00431	CUB domain (CUB)	CUB domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	Gastric intrinsic factor	vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding protein binding cargo receptor ligand activity	localization nitrogen compound transport transport vitamin transport organic substance transport cobalamin transport establishment of localization monoatomic ion transmembrane transport inorganic ion transmembrane transport metal ion transport inorganic cation transmembrane transport cobalt ion transport transmembrane transport monoatomic cation transmembrane transport localization nitrogen compound transport transport vitamin transport organic substance transport cobalamin transport establishment of localization monoatomic ion transmembrane transport inorganic ion transmembrane transport metal ion transport inorganic cation transmembrane transport cobalt ion transport transmembrane transport monoatomic cation transmembrane transport transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport	cell projection actin-based cell projection microvillus cellular anatomical entity plasma membrane bounded cell projection cell periphery apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure endosome cell projection actin-based cell projection microvillus cellular anatomical entity plasma membrane bounded cell projection cell periphery apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle extracellular region extracellular space lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole lysosomal lumen intracellular organelle lumen organelle lumen lysosome
B, D, F	Cubilin	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity vitamin binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding cargo receptor activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity vitamin binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding cargo receptor activity identical protein binding protein binding protein homodimerization activity protein dimerization activity	organic hydroxy compound metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process primary metabolic process organic cyclic compound metabolic process secondary alcohol metabolic process organic substance metabolic process small molecule metabolic process metabolic process lipid metabolic process localization cellular localization organic hydroxy compound metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process primary metabolic process organic cyclic compound metabolic process secondary alcohol metabolic process organic substance metabolic process small molecule metabolic process metabolic process lipid metabolic process localization cellular localization establishment of localization in cell cellular process establishment of localization protein localization establishment of protein localization nitrogen compound transport transport organic substance transport lipoprotein transport protein transport cellular macromolecule localization macromolecule localization lipoprotein localization cobalamin metabolic process organonitrogen compound metabolic process tetrapyrrole metabolic process water-soluble vitamin metabolic process vitamin metabolic process vitamin transport cobalamin transport biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus multicellular organismal process multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis import into cell receptor-mediated endocytosis endocytosis vesicle-mediated transport	clathrin-coated pit membrane cellular anatomical entity endomembrane system cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen clathrin-coated pit membrane cellular anatomical entity endomembrane system cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol plasma membrane bounded cell projection cell projection actin-based cell projection microvillus microvillus membrane cell projection membrane intracellular vesicle cytoplasmic vesicle endocytic vesicle protein-containing complex receptor complex vacuolar membrane lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane Golgi apparatus endosome brush border membrane cluster of actin-based cell projections brush border extrinsic component of plasma membrane cell surface extrinsic component of external side of plasma membrane extrinsic component of membrane external side of plasma membrane side of membrane endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR002157	Cobalamin (vitamin B12)-binding protein	Family
B, D, F	IPR024731	EGF domain	Domain
B, D, F	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
B, D, F	IPR035914	Spermadhesin, CUB domain superfamily	Homologous Superfamily
B, D, F	IPR000859	CUB domain	Domain
B, D, F	IPR000742	EGF-like domain	Domain
B, D, F	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
B, D, F	IPR001881	EGF-like calcium-binding domain	Domain
B, D, F	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E	Pharos: P27352	congenital intrinsic factor deficiency schizophrenia bipolar disorder Crohn disease Congenital deficiency of intrinsic factor pernicious anemia
B, D, F	Pharos: O60494	melanoma megaloblastic anemia amphetamine abuse Imerslund-Grasbeck syndrome type 1 colorectal cancer Cytopenia proteinuria congenital anemia Dent disease nephrosclerosis cutaneous melanoma osteosarcoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.